The effect of curcumin on the stability of Aβ dimers Li Na Zhao, See-Wing Chiu, Jérôme Benoit, Lock Yue Chew,, and Yuguang Mu, School of Physical and Mathematical Sciences, Nanyang Technological University, Beckman Institute, University of Illinois, Urbana, Illinois, and School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore E-mail: lockyue@ntu.edu.sg; ygmu@ntu.edu.sg To whom correspondence should be addressed Nanyang Technological University University of Illinois Nanyang Technological University S1
Figure S1: The snapshot of the dimer at the end of the set 2 simulation. The dimer was represented as cartoon (β-sheet: yellow; helix: purple; for the others from peptide A: tv_green; for the others from pepitde B: tv_blue). S2
Figure S2: The initial M0-10 models. The secondary structure of dimer was represented as transparent cartoon (β -sheet: yellow; α-helix: purple; others for peptide A: tv_blue; others for peptide B: tv_green). The curcumin was shown as stick and colored by element (C: yellow; H: grey; O: red). For the residues from peptide A involved in the contacts with curcumin was represented as stick and colored by element (C: marine; N: blue; H: grey; O: red). For the residues from peptide B involved in the direct contact with curcumin was also represented as stick and colored by the similar element except C atom was colore as green to distinguish from peptide A. Please note for those Cα atom exits in the β -sheet part was colored as yellow, and purple for the Cα atom in α-helix part. S3
Figure S3: The initial M11-20 models. The secondary structure of dimer was represented as transparent cartoon (β -sheet: yellow; α-helix: purple; others for peptide A: tv_blue; others for peptide B: tv_green). The curcumin was shown as stick and colored by element (C: yellow; H: grey; O: red). For the residues from peptide A involved in the contacts with curcumin was represented as stick and colored by element (C: marine; N: blue; H: grey; O: red). For the residues from peptide B involved in the direct contact with curcumin was also represented as stick and colored by the similar element except C atom was colore as green to distinguish from peptide A. Please note for those Cα atom exits in the β -sheet part was colored as yellow, and purple for the Cα atom in α-helix part. S4
Table S1: Calculated pka value for titratable residues. Residues pka values N-terminus 7.9 AspNT 2.4 Glu-3 4.2 Arg-5 12.2 His-6 6.0 Asp-7 4.2 Tyr-10 11.0 Glu-11 4.6 His-13 5.5 His-14 7.6 Lys-16 9.7 Glu-22 4.5 Asp-23 4.4 Lys-28 10.3 C-terminus 4.4 S5
Figure S4: Evolution of the secondary structure of protein in the presence of keto-enol conformers and the controlled group M0. S6
Table S2: Simulation System β-diketone tautomers keto-enol tautomers Binding Energy Binding Energy Model ID Potential binding sites Rank Water molecules Model ID Potential binding sites Rank Water molecules kcal/mol kcal/mol M1 M2 A: LEU-34 A: LEU-34, ILE-32-3.84 5 7475 M11 B :HIS-14 α, PHE-19 β B: HIS-14 α A: VAL-12 B: ILE-32-5.30 1 7471 M12 β, LEU-34 B: ARG-5, ALA-21 β MET-35 β M3 A: PHE-20, VAL-39-2.82 9 7477 M13 M4-4.38 1 8111-4.14 2 7472 A: LEU-17, PHE-19 β -3.74 3 7474 VAL-39 B: ARG-5, ALA-21 β -3.04 8 7480 M14 B: GLY-38, VAL-40 β -3.71 4 7478 GLY-38 β, VAL-40 M5 B: HIS-14 α, LEU-17 B: GLU-3, HIS-6-4.37 3 7478 M15 PHE-19 SER-8 B: ILE-32 β, LEU-34 B: ILE-32 β, LEU-34 M6-3.08 7 7474 M16 MET-35 β MET-35 β A: HIS-14 α, LEU-17 M7 A: LEU-17, PHE-19 β -4.79 2 7469 M17 PHE-19 β, ALA-21 α M8 A: ARG-5, VAL-12-2.76 10 7472 M18 A: TYR-10, VAL-12 B: GLU-3 A: ALA-2 β, PHE-4 M9 B: ARG-5-4.04 4 7466 M19 ARG-5, HIS-16 M10 A: HIS-14, LEU-17 A: ASP-7-3.66 6 7469 M20 PHE-19 B: GLY-25 β M0 - - - 7495 - indicates NULL. α indicates residue sites on α-helix. β indicates residue sites on β-sheet. -3.55 5 7468-3.53 6 7479-2.97 7 7475-2.88 8 7471-2.77 9 7475-2.50 10 7471 S7
Figure S5: Time evolution of the number of residues in β-structure (β-sheet and β-bridge) of peptide A (black line) and B (colored by red) and the contact numbers between peptide A and B (colored by magenta). The data were extracted from each 11 model trajectories and averaged per 4 ns. The contact number were divided by 100. S8
Figure S6: The secondary structure propensity of Aβ residues in the presence and absence of curcumin. S9
Figure S7: The π-π stacking propensity of Aβ residues His, Tyr and Phe with curcumin R1 and R2 respectively. S10
Table S3: The occurence of dehydron. The occurence of dehydron pairs occurence B: (24V, 27N) 292 A: (24V, 27N) 222 B: (11E, 15Q) 157 B: (34L, 41I) 150 (A: 40V, B: 28K) 133 A:(30A, 37G) 124 A:(11E, 15Q) 110 B:(12V, 16K) 98 A:(22E, 29G) 89 A:(12V, 16K) 53 B:(22E, 29G) 52 A:(6H, 12V) 51 (A:38G, B:41I) 49 A:(23D, 27N) 45 A:(23D, 28K) 44 A:(5R, 9D) 42 (A:36V, B:39V) 37 B:(1D, 15Q) 35 A:(22E, 27N) 35 (A:3E, B:24V) 34 (A:41I, B:28K) 33 (A:1D, B:26S) 32 (A:1D, B:27N) 31 A:(7D, 10Y) 31 A:(28K, 35G) 31... < 30 S11
[ moleculetype ] ; Name nrexcl CUR 3 Table S4: The curcumin topology [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 CUR C21 1 0.200 15.0350 2 OA 1 CUR O4 1-0.400 15.9994 3 C 1 CUR C19 1 0.200 12.0110 4 CR1 1 CUR C20 1-0.060 12.0110 5 HC 1 CUR H20 1 0.060 1.0080 6 C 1 CUR C18 1 0.265 12.0110 7 OA 1 CUR O5 1-0.683 15.9994 8 H 1 CUR H52 1 0.418 1.0080 9 CR1 1 CUR C17 2-0.060 12.0110 10 HC 1 CUR H17 2 0.060 1.0080 11 CR1 1 CUR C16 2-0.060 12.0110 12 HC 1 CUR H16 2 0.060 1.0080 13 C 1 CUR C15 2-0.000 12.0110 14 C 1 CUR C14 3 0.000 13.0190 15 C 1 CUR C13 3 0.000 13.0190 16 C 1 CUR C12 3 0.265 12.0110 17 OA 1 CUR O3 3-0.683 15.9994 18 H 1 CUR H32 3 0.418 1.0080 19 C 1 CUR C11 3 0.000 13.0190 20 C 1 CUR C10 3 0.265 12.0110 21 O 1 CUR O6 3-0.265 15.9994 22 C 1 CUR C9 4 0.000 13.0190 23 C 1 CUR C8 4 0.000 13.0190 24 C 1 CUR C4 4-0.000 12.0110 25 CR1 1 CUR C3 4-0.060 12.0110 26 HC 1 CUR H31 4 0.060 1.0080 27 CR1 1 CUR C5 5-0.060 12.0110 28 HC 1 CUR H51 5 0.060 1.0080 29 CR1 1 CUR C6 6-0.060 12.0110 30 HC 1 CUR H6 6 0.060 1.0080 31 C 1 CUR C7 6 0.265 12.0110 32 OA 1 CUR O2 6-0.683 15.9994 33 H 1 CUR H22 6 0.418 1.0080 34 C 1 CUR C2 6 0.200 12.0110 35 OA 1 CUR O1 6-0.400 15.9994 36 CH3 1 CUR C1 6 0.200 15.0350 [ bonds ] ; ai aj fu c0, c1,... 2 1 2 0.143 8180000.0 0.143 8180000.0 ; O4 C21 3 2 2 0.136 10200000.0 0.136 10200000.0 ; C19 O4 3 4 2 0.139 10800000.0 0.139 10800000.0 ; C19 C20 3 6 2 0.139 10800000.0 0.139 10800000.0 ; C19 C18 4 5 2 0.109 12300000.0 0.109 12300000.0 ; C20 H20 13 4 2 0.139 10800000.0 0.139 10800000.0 ; C15 C20 6 7 2 0.136 10200000.0 0.136 10200000.0 ; C18 O5 6 9 2 0.139 10800000.0 0.139 10800000.0 ; C18 C17 7 8 2 0.100 15700000.0 0.100 15700000.0 ; O5 H52 9 10 2 0.109 12300000.0 0.109 12300000.0 ; C17 H17 9 11 2 0.139 10800000.0 0.139 10800000.0 ; C17 C16 11 12 2 0.109 12300000.0 0.109 12300000.0 ; C16 H16 13 11 2 0.139 10800000.0 0.139 10800000.0 ; C15 C16 13 14 2 0.139 10800000.0 0.139 10800000.0 ; C15 C14 14 15 2 0.153 7150000.0 0.153 7150000.0 ; C14 C13 16 15 2 0.153 7150000.0 0.153 7150000.0 ; C12 C13 16 17 2 0.136 10200000.0 0.136 10200000.0 ; C12 O3 16 19 2 0.153 7150000.0 0.153 7150000.0 ; C12 C11 17 18 2 0.100 15700000.0 0.100 15700000.0 ; O3 H32 20 19 2 0.153 7150000.0 0.153 7150000.0 ; C10 C11 20 21 2 0.123 16600000.0 0.123 16600000.0 ; C10 O6 20 22 2 0.153 7150000.0 0.153 7150000.0 ; C10 C9 22 23 2 0.153 7150000.0 0.153 7150000.0 ; C9 C8 24 23 2 0.139 10800000.0 0.139 10800000.0 ; C4 C8 24 25 2 0.139 10800000.0 0.139 10800000.0 ; C4 C3 24 27 2 0.139 10800000.0 0.139 10800000.0 ; C4 C5 25 26 2 0.109 12300000.0 0.109 12300000.0 ; C3 H31 S12
34 25 2 0.139 10800000.0 0.139 10800000.0 ; C2 C3 27 28 2 0.109 12300000.0 0.109 12300000.0 ; C5 H51 27 29 2 0.139 10800000.0 0.139 10800000.0 ; C5 C6 29 30 2 0.109 12300000.0 0.109 12300000.0 ; C6 H6 31 29 2 0.139 10800000.0 0.139 10800000.0 ; C7 C6 31 32 2 0.136 10200000.0 0.136 10200000.0 ; C7 O2 31 34 2 0.139 10800000.0 0.139 10800000.0 ; C7 C2 32 33 2 0.100 15700000.0 0.100 15700000.0 ; O2 H22 34 35 2 0.136 10200000.0 0.136 10200000.0 ; C2 O1 35 36 2 0.143 8180000.0 0.143 8180000.0 ; O1 C1 [ pairs ] ; ai aj fu c0, c1,... 1 4 1 ; C21 C20 1 6 1 ; C21 C18 2 5 1 ; O4 H20 2 7 1 ; O4 O5 2 9 1 ; O4 C17 2 13 1 ; O4 C15 3 8 1 ; C19 H52 3 10 1 ; C19 H17 3 11 1 ; C19 C16 3 14 1 ; C19 C14 4 7 1 ; C20 O5 4 9 1 ; C20 C17 4 12 1 ; C20 H16 4 15 1 ; C20 C13 5 6 1 ; H20 C18 5 11 1 ; H20 C16 5 14 1 ; H20 C14 6 12 1 ; C18 H16 6 13 1 ; C18 C15 7 10 1 ; O5 H17 7 11 1 ; O5 C16 8 9 1 ; H52 C17 9 14 1 ; C17 C14 10 12 1 ; H17 H16 10 13 1 ; H17 C15 11 15 1 ; C16 C13 12 14 1 ; H16 C14 13 16 1 ; C15 C12 14 17 1 ; C14 O3 14 19 1 ; C14 C11 15 18 1 ; C13 H32 15 20 1 ; C13 C10 16 21 1 ; C12 O6 16 22 1 ; C12 C9 17 20 1 ; O3 C10 18 19 1 ; H32 C11 19 23 1 ; C11 C8 20 24 1 ; C10 C4 21 23 1 ; O6 C8 22 25 1 ; C9 C3 22 27 1 ; C9 C5 23 26 1 ; C8 H31 23 28 1 ; C8 H51 23 29 1 ; C8 C6 23 34 1 ; C8 C2 24 30 1 ; C4 H6 24 31 1 ; C4 C7 24 35 1 ; C4 O1 25 28 1 ; C3 H51 25 29 1 ; C3 C6 25 32 1 ; C3 O2 25 36 1 ; C3 C1 26 27 1 ; H31 C5 26 31 1 ; H31 C7 26 35 1 ; H31 O1 27 32 1 ; C5 O2 27 34 1 ; C5 C2 28 30 1 ; H51 H6 28 31 1 ; H51 C7 29 33 1 ; C6 H22 29 35 1 ; C6 O1 S13
30 32 1 ; H6 O2 30 34 1 ; H6 C2 31 36 1 ; C7 C1 32 35 1 ; O2 O1 33 34 1 ; H22 C2 [ angles ] ; ai aj ak fu c0, c1,... 1 2 3 2 109.5 380.0 109.5 380.0 ; C21 O4 C19 2 3 4 2 120.0 560.0 120.0 560.0 ; O4 C19 C20 2 3 6 2 115.0 610.0 115.0 610.0 ; O4 C19 C18 4 3 6 2 120.0 560.0 120.0 560.0 ; C20 C19 C18 3 4 5 2 120.0 505.0 120.0 505.0 ; C19 C20 H20 3 4 13 2 120.0 505.0 120.0 505.0 ; C19 C20 C15 5 4 13 2 120.0 505.0 120.0 505.0 ; H20 C20 C15 3 6 7 2 115.0 610.0 115.0 610.0 ; C19 C18 O5 3 6 9 2 120.0 560.0 120.0 560.0 ; C19 C18 C17 7 6 9 2 120.0 560.0 120.0 560.0 ; O5 C18 C17 6 7 8 2 109.5 450.0 109.5 450.0 ; C18 O5 H52 6 9 10 2 120.0 505.0 120.0 505.0 ; C18 C17 H17 6 9 11 2 120.0 505.0 120.0 505.0 ; C18 C17 C16 10 9 11 2 120.0 505.0 120.0 505.0 ; H17 C17 C16 9 11 12 2 120.0 505.0 120.0 505.0 ; C17 C16 H16 9 11 13 2 120.0 505.0 120.0 505.0 ; C17 C16 C15 12 11 13 2 120.0 505.0 120.0 505.0 ; H16 C16 C15 4 13 11 2 120.0 560.0 120.0 560.0 ; C20 C15 C16 4 13 14 2 120.0 560.0 120.0 560.0 ; C20 C15 C14 11 13 14 2 120.0 560.0 120.0 560.0 ; C16 C15 C14 13 14 15 2 115.0 610.0 115.0 610.0 ; C15 C14 C13 14 15 16 2 115.0 610.0 115.0 610.0 ; C14 C13 C12 15 16 17 2 115.0 610.0 115.0 610.0 ; C13 C12 O3 15 16 19 2 115.0 610.0 115.0 610.0 ; C13 C12 C11 17 16 19 2 115.0 610.0 115.0 610.0 ; O3 C12 C11 16 17 18 2 109.5 450.0 109.5 450.0 ; C12 O3 H32 16 19 20 2 115.0 610.0 115.0 610.0 ; C12 C11 C10 19 20 21 2 121.0 685.0 121.0 685.0 ; C11 C10 O6 19 20 22 2 115.0 610.0 115.0 610.0 ; C11 C10 C9 21 20 22 2 121.0 685.0 121.0 685.0 ; O6 C10 C9 20 22 23 2 115.0 610.0 115.0 610.0 ; C10 C9 C8 22 23 24 2 115.0 610.0 115.0 610.0 ; C9 C8 C4 23 24 25 2 120.0 560.0 120.0 560.0 ; C8 C4 C3 23 24 27 2 120.0 560.0 120.0 560.0 ; C8 C4 C5 25 24 27 2 120.0 560.0 120.0 560.0 ; C3 C4 C5 24 25 26 2 120.0 505.0 120.0 505.0 ; C4 C3 H31 24 25 34 2 120.0 505.0 120.0 505.0 ; C4 C3 C2 26 25 34 2 120.0 505.0 120.0 505.0 ; H31 C3 C2 24 27 28 2 120.0 505.0 120.0 505.0 ; C4 C5 H51 24 27 29 2 120.0 505.0 120.0 505.0 ; C4 C5 C6 28 27 29 2 120.0 505.0 120.0 505.0 ; H51 C5 C6 27 29 30 2 120.0 505.0 120.0 505.0 ; C5 C6 H6 27 29 31 2 120.0 505.0 120.0 505.0 ; C5 C6 C7 30 29 31 2 120.0 505.0 120.0 505.0 ; H6 C6 C7 29 31 32 2 120.0 560.0 120.0 560.0 ; C6 C7 O2 29 31 34 2 120.0 560.0 120.0 560.0 ; C6 C7 C2 32 31 34 2 115.0 610.0 115.0 610.0 ; O2 C7 C2 31 32 33 2 109.5 450.0 109.5 450.0 ; C7 O2 H22 25 34 31 2 120.0 560.0 120.0 560.0 ; C3 C2 C7 25 34 35 2 120.0 560.0 120.0 560.0 ; C3 C2 O1 31 34 35 2 115.0 610.0 115.0 610.0 ; C7 C2 O1 34 35 36 2 109.5 380.0 109.5 380.0 ; C2 O1 C1 [ dihedrals ] ; ai aj ak al fu c0, c1, m,... 3 2 4 6 2 0.0 167.4 0.0 167.4 ; imp C19 O4 C20 C18 4 3 13 5 2 0.0 167.4 0.0 167.4 ; imp C20 C19 C15 H20 6 9 7 3 2 0.0 167.4 0.0 167.4 ; imp C18 C17 O5 C19 9 6 11 10 2 0.0 167.4 0.0 167.4 ; imp C17 C18 C16 H17 11 9 13 12 2 0.0 167.4 0.0 167.4 ; imp C16 C17 C15 H16 13 14 11 4 2 0.0 167.4 0.0 167.4 ; imp C15 C14 C16 C20 16 19 17 15 2 0.0 167.4 0.0 167.4 ; imp C12 C11 O3 C13 20 22 21 19 2 0.0 167.4 0.0 167.4 ; imp C10 C9 O6 C11 24 23 27 25 2 0.0 167.4 0.0 167.4 ; imp C4 C8 C5 C3 25 24 34 26 2 0.0 167.4 0.0 167.4 ; imp C3 C4 C2 H31 27 24 29 28 2 0.0 167.4 0.0 167.4 ; imp C5 C4 C6 H51 S14
29 27 31 30 2 0.0 167.4 0.0 167.4 ; imp C6 C5 C7 H6 31 29 32 34 2 0.0 167.4 0.0 167.4 ; imp C7 C6 O2 C2 34 25 35 31 2 0.0 167.4 0.0 167.4 ; imp C2 C3 O1 C7 3 4 13 11 2 0.0 209.3 0.0 209.3 ; imp C19 C20 C15 C16 4 13 11 9 2 0.0 209.3 0.0 209.3 ; imp C20 C15 C16 C17 13 11 9 6 2 0.0 209.3 0.0 209.3 ; imp C15 C16 C17 C18 11 9 6 3 2 0.0 209.3 0.0 209.3 ; imp C16 C17 C18 C19 9 6 3 4 2 0.0 209.3 0.0 209.3 ; imp C17 C18 C19 C20 6 3 4 13 2 0.0 209.3 0.0 209.3 ; imp C18 C19 C20 C15 24 25 34 31 2 0.0 209.3 0.0 209.3 ; imp C4 C3 C2 C7 25 34 31 29 2 0.0 209.3 0.0 209.3 ; imp C3 C2 C7 C6 34 31 29 27 2 0.0 209.3 0.0 209.3 ; imp C2 C7 C6 C5 31 29 27 24 2 0.0 209.3 0.0 209.3 ; imp C7 C6 C5 C4 29 27 24 25 2 0.0 209.3 0.0 209.3 ; imp C6 C5 C4 C3 27 24 25 34 2 0.0 209.3 0.0 209.3 ; imp C5 C4 C3 C2 6 3 2 1 1 180.0 16.7 2 180.0 16.7 2 ; dih C18 C19 O4 C21 3 6 7 8 1 180.0 7.1 2 180.0 7.1 2 ; dih C19 C18 O5 H52 15 14 13 4 1 180.0 5.9 2 180.0 5.9 2 ; dih C13 C14 C15 C20 16 15 14 13 1 180.0 5.9 2 180.0 5.9 2 ; dih C12 C13 C14 C15 19 16 15 14 1 180.0 5.9 2 180.0 5.9 2 ; dih C11 C12 C13 C14 15 16 17 18 1 180.0 16.7 2 180.0 16.7 2 ; dih C13 C12 O3 H32 20 19 16 15 1 180.0 5.9 2 180.0 5.9 2 ; dih C10 C11 C12 C13 22 20 19 16 1 180.0 5.9 2 180.0 5.9 2 ; dih C9 C10 C11 C12 23 22 20 19 1 180.0 5.9 2 180.0 5.9 2 ; dih C8 C9 C10 C11 24 23 22 20 1 180.0 5.9 2 180.0 5.9 2 ; dih C4 C8 C9 C10 27 24 23 22 1 180.0 5.9 2 180.0 5.9 2 ; dih C5 C4 C8 C9 29 31 32 33 1 180.0 7.1 2 180.0 7.1 2 ; dih C6 C7 O2 H22 25 34 35 36 1 180.0 16.7 2 180.0 16.7 2 ; dih C3 C2 O1 C1 S15